So I was playing Skyward Sword months ago running full speed on the same PC (Except I had a GTX 560 and an older revision) and now I'm barely cutting 24 FPS now. What the heck happened? Same thing goes with Metroid Prime 2 (Trilogy), which I also configured to run at full speed, now it runs at about 80%. I even get stutters in Brawl. Can anyone provide some insight here? I figured it might be a hardware issue so I posted this here, although I'm not sure. If it belongs somewhere else, I am sorry.

@CryZENx Your CPU is much faster than his CPU clock for clock . i5 4670k / i7 4770k stock speed is as fast as i5 3570k @ 4.2GHz / i5 2500k @ 4.4GHz
i5 4670k / i7 4770k @ 4.2GHz is faster than i5 2500k @ 5.3GHz in Dolphin ! See Dolphin Benchmark :https://forums.dolphin-emu.org/Thread-the-legend-of-zelda-the-wind-waker-cpu-benchmark
@Zell1226 Latest Dolphin uses the new AX HLE which is more demanding than the old HLE . Not mention Dolphin aims for accuracy and accuracy = who cares about performance anyway
Try :
_Right-click the game - Properties - Tick "Vbeam Speed Hack"
_Set Framelimit = 30 or 60(depending on the game) and tick "limit by FPS" instead of auto
_If you still not get full speed , overclock i5 2500k to 4.8GHz
_The new AX HLE is almost the same as LLE . If you not run game at full speed , you will game stuttering audio . You can fix this by using Vbeam trick : tick Vbeam and untick Idle Skipping

His GPU is likely throttling. He upgraded to a 700 series gpu. He needs to go into nvidia control panel and force the power mode to "prefer maximum performance". I'll let someone else explain how to do it because I've already explained it so many times (or just google it).

"Normally if given a choice between doing something and nothing, I’d choose to do nothing. But I would do something if it helps someone else do nothing. I’d work all night if it meant nothing got done."
-Ron Swanson

"I shall be a good politician, even if it kills me. Or if it kills anyone else for that matter. "
-Mark Antony

I should also point out that your build is horribly out of date and not from the official site.

"Normally if given a choice between doing something and nothing, I’d choose to do nothing. But I would do something if it helps someone else do nothing. I’d work all night if it meant nothing got done."
-Ron Swanson

"I shall be a good politician, even if it kills me. Or if it kills anyone else for that matter. "
-Mark Antony

Are you forcing the GPU into high power mode in catalyst control panel?

"Normally if given a choice between doing something and nothing, I’d choose to do nothing. But I would do something if it helps someone else do nothing. I’d work all night if it meant nothing got done."
-Ron Swanson

"I shall be a good politician, even if it kills me. Or if it kills anyone else for that matter. "
-Mark Antony